I want to simulate a circuit consisting of PowerPC processor and FPGAs
as main components. Is it possible to verify the schematic and
functionality of all the components in some CAD tool before getting
all the things stuffed on PCB? What tools can do this job?

You can verify the schematic/PCB connectivity with a a Design Rule
Check(DRC).
FPGA functionality can be checked with the likes of ModelSim, but
that's getting very complex indeed, and if you have to ask the
question then I doubt you posses the skills to do it.
You basically can't "simulate" such a system as a whole, only various
parts of it.